This article aims to explore the formation of sanitary administrative system in Taiwan, centering on the sanitary administrative system and the structural change inside its organization. Also, it attempts to figure out the characteristics of sanitary administrative system in Taiwan, from the perspective of a comparison with the modern sanitary administrative system in Japan. In fact, this study shows several results. First, in Taiwanese local sanitary administration only the police administration was in charge of the sanitary administration, and there was no other authority took charge of it except the chiefs of local governments. Second, in Meiji 34th (1901), after the reform of administrative organization, the central sanitary administration was conducted by the Police Department of Civil Department of Taiwan Governor-General. Third, due to police officers were assigned in the Police Department, the central sanitary administration in Taiwan was not only a supervisory authority but also an implementing one. Fourth, the Police Department utilized the police command system through the local governments to the bottom administration. It made the sanitary administration transform into a unitary system which could penetrate the bottom society. Therefore, it could be said that Meiji 34TH is a significant turning point of sanitary administrative system in Taiwan. Likewise, it shows that the sanitary administrative authority in Taiwan possessed bigger power to supervise and implement the sanitary administration.